Taming Message-Passing Communication in Compositional Reasoning About Confidentiality

2017 ◽  
pp. 45-66 ◽  
Author(s):  
Ximeng Li ◽  
Heiko Mantel ◽  
Markus Tasch
Keyword(s):  
Message Passing ◽  
Compositional Reasoning

Transactional events

2008 ◽  
Vol 18 (5-6) ◽  
pp. 649-706 ◽  
Author(s):  
KEVIN DONNELLY ◽  
MATTHEW FLUET
Keyword(s):  
Message Passing ◽  
Formal Semantics ◽  
Concurrent Programming ◽  
Expressive Power ◽  
Detailed Account ◽  
Concurrent Programs ◽  
Compositional Reasoning ◽  
Compositional Structure ◽  
High Level

AbstractConcurrent programs require high-level abstractions in order to manage complexity and enable compositional reasoning. In this paper, we introduce a novel concurrency abstraction, dubbed transactional events, which combines first-class synchronous message passing events with all-or-nothing transactions. This combination enables simple solutions to interesting problems in concurrent programming. For example, guarded synchronous receive can be implemented as an abstract transactional event, whereas in other languages it requires a non-abstract, non-modular protocol. As another example, three-way rendezvous can be implemented as an abstract transactional event, which is impossible using first-class events alone. Both solutions are easy to code and easy to reason about.The expressive power of transactional events arises from a sequencing combinator whose semantics enforces an all-or-nothing transactional property – either both of the constituent events synchronize in sequence or neither of them synchronizes. This sequencing combinator, along with a non-deterministic choice combinator, gives transactional events the compositional structure of a monad-with-plus. We provide a formal semantics for transactional events and give a detailed account of an implementation.

Message Passing Neural Networks for Partial Charge Assignment to Metal-Organic Frameworks

2020 ◽  
Author(s):  
Ali Raza ◽  
Arni Sturluson ◽  
Cory Simon ◽  
Xiaoli Fern
Keyword(s):  
Electronic Structure ◽  
Message Passing ◽  
Gas Adsorption ◽  
Metal Organic Frameworks ◽  
Computational Cost ◽  
Electronic Structure Calculations ◽  
High Fidelity ◽  
Partial Charges ◽  
Metal Organic ◽  
Structure Calculations

Virtual screenings can accelerate and reduce the cost of discovering metal-organic frameworks (MOFs) for their applications in gas storage, separation, and sensing. In molecular simulations of gas adsorption/diffusion in MOFs, the adsorbate-MOF electrostatic interaction is typically modeled by placing partial point charges on the atoms of the MOF. For the virtual screening of large libraries of MOFs, it is critical to develop computationally inexpensive methods to assign atomic partial charges to MOFs that accurately reproduce the electrostatic potential in their pores. Herein, we design and train a message passing neural network (MPNN) to predict the atomic partial charges on MOFs under a charge neutral constraint. A set of ca. 2,250 MOFs labeled with high-fidelity partial charges, derived from periodic electronic structure calculations, serves as training examples. In an end-to-end manner, from charge-labeled crystal graphs representing MOFs, our MPNN machine-learns features of the local bonding environments of the atoms and learns to predict partial atomic charges from these features. Our trained MPNN assigns high-fidelity partial point charges to MOFs with orders of magnitude lower computational cost than electronic structure calculations. To enhance the accuracy of virtual screenings of large libraries of MOFs for their adsorption-based applications, we make our trained MPNN model and MPNN-charge-assigned computation-ready, experimental MOF structures publicly available.<br>

Building Attention and Edge Convolution Neural Networks for Bioactivity and Physical-Chemical Property Prediction

2019 ◽  
Author(s):  
Michael Withnall ◽  
Edvard Lindelöf ◽  
Ola Engkvist ◽  
Hongming Chen
Keyword(s):  
Message Passing ◽  
State Of The Art ◽  
A Priori ◽  
Model Performance ◽  
Learning Approaches ◽  
Physical Chemical ◽  
Chemical Descriptor ◽  
Derived Properties ◽  
Memory Schemes ◽  
Hyperparameter Selection

We introduce Attention and Edge Memory schemes to the existing Message Passing Neural Network framework for graph convolution, and benchmark our approaches against eight different physical-chemical and bioactivity datasets from the literature. We remove the need to introduce <i>a priori</i> knowledge of the task and chemical descriptor calculation by using only fundamental graph-derived properties. Our results consistently perform on-par with other state-of-the-art machine learning approaches, and set a new standard on sparse multi-task virtual screening targets. We also investigate model performance as a function of dataset preprocessing, and make some suggestions regarding hyperparameter selection.

Multi-level Parallelization of Genotype Imputation on Supercomputers

2020 ◽  
Vol 15 ◽  
Author(s):  
Weiwen Zhang ◽  
Long Wang ◽  
Theint Theint Aye ◽  
Juniarto Samsudin ◽  
Yongqing Zhu
Keyword(s):  
Association Study ◽  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Genome Wide Association Study ◽  
Job Scheduling ◽  
Genotype Imputation ◽  
Job Level ◽  
Multi Level ◽  
High Performance Requirement

Background: Genotype imputation as a service is developed to enable researchers to estimate genotypes on haplotyped data without performing whole genome sequencing. However, genotype imputation is computation intensive and thus it remains a challenge to satisfy the high performance requirement of genome wide association study (GWAS). Objective: In this paper, we propose a high performance computing solution for genotype imputation on supercomputers to enhance its execution performance. Method: We design and implement a multi-level parallelization that includes job level, process level and thread level parallelization, enabled by job scheduling management, message passing interface (MPI) and OpenMP, respectively. It involves job distribution, chunk partition and execution, parallelized iteration for imputation and data concatenation. Due to the design of multi-level parallelization, we can exploit the multi-machine/multi-core architecture to improve the performance of genotype imputation. Results: Experiment results show that our proposed method can outperform the Hadoop-based implementation of genotype imputation. Moreover, we conduct the experiments on supercomputers to evaluate the performance of the proposed method. The evaluation shows that it can significantly shorten the execution time, thus improving the performance for genotype imputation. Conclusion: The proposed multi-level parallelization, when deployed as an imputation as a service, will facilitate bioinformatics researchers in Singapore to conduct genotype imputation and enhance the association study.

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